U.S. patent application number 11/968078 was filed with the patent office on 2008-07-24 for membrane-based assays.
This patent application is currently assigned to Synamem Corporation. Invention is credited to John T. Groves, Robert J. Schafer, Morrison Ulman, Victoria Yamazaki.
Application Number | 20080176759 11/968078 |
Document ID | / |
Family ID | 31994083 |
Filed Date | 2008-07-24 |
United States Patent
Application |
20080176759 |
Kind Code |
A1 |
Yamazaki; Victoria ; et
al. |
July 24, 2008 |
Membrane-based assays
Abstract
Membrane-based assays using surface detector array devices
suitable for use with a biosensor are disclosed. The device is
formed of a substrate having a surface defining a plurality of
distinct bilayer-compatible surface regions separated by one or
more bilayer barrier regions. The bilayer-compatible surface
regions carry on them, separated by an aqueous film, supported
fluid bilayers. The bilayers may contain selected receptors or
biomolecules. A bulk aqueous phase covers the bilayers on the
substrate surface. Arrays may be engineered to display natural
membrane materials in a native fluid bilayer configuration,
permitting high-throughput discovery of drugs that target and
affect membrane components. The membrane-based assays detect
binding events by monitoring binding-induced changes in one or more
physical properties of fluid bilayers.
Inventors: |
Yamazaki; Victoria; (San
Francisco, CA) ; Schafer; Robert J.; (Sacramento,
CA) ; Ulman; Morrison; (Mountain View, CA) ;
Groves; John T.; (Berkeley, CA) |
Correspondence
Address: |
PERKINS COIE LLP
P.O. BOX 2168
MENLO PARK
CA
94026
US
|
Assignee: |
Synamem Corporation
Burlingame
CA
|
Family ID: |
31994083 |
Appl. No.: |
11/968078 |
Filed: |
December 31, 2007 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10661790 |
Sep 11, 2003 |
|
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11968078 |
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60410173 |
Sep 11, 2002 |
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Current U.S.
Class: |
506/9 |
Current CPC
Class: |
G01N 33/554 20130101;
C12Q 1/18 20130101; G01N 33/54373 20130101; C40B 30/04 20130101;
G01N 2500/00 20130101 |
Class at
Publication: |
506/9 |
International
Class: |
C40B 30/04 20060101
C40B030/04 |
Claims
1. A method for assaying an interaction between a test agent and a
lipid bilayer-associated component, comprising: providing a surface
detector array device comprising (i) a substrate having a surface
defining a plurality of distinct bilayer-compatible surface regions
separated by one or more bilayer barrier regions, said
bilayer-compatible surface regions and said bilayer barrier regions
being formed of different materials, and (ii) a plurality of lipid
bilayer expanses localized above said plurality of distinct
bilayer-compatible surface regions, wherein said lipid bilayer
expanses are localized above said surface regions in the absence of
covalent linkages between said lipid bilayer expanses and said
bilayer-compatible surface regions, and are separated therefrom by
an aqueous film interposed between said bilayer-compatible surface
regions and said corresponding lipid bilayer expanses, the lipid
bilayer expanses having a component associated with the lipid
bilayer expanse; contacting said device with a bulk aqueous phase
comprising the test agent that specifically binds to the lipid
bilayer-associated component evaluating the acyl chain mobility of
one or more of said lipid bilayer expanses, whereby the acyl chain
mobility changes when said test agent binds to said lipid
bilayer-associated component; and detecting binding of the test
agent to the lipid bilayer-associated component by correlating a
change in acyl chain mobility to binding.
2. The method of claim 1, wherein said evaluating acyl chain
mobility comprises using at least one of Fourier-transformed
infrared spectroscopy, sum frequency generation spectroscopy,
surface reflective spectroscopy, surface plasmon spectroscopy, and
imaging ellipsometry to determine acyl chain mobility.
3. The method of claim 1, wherein the lipid bilayer-associated
component is selected from a protein, a nucleic acid, a glycolipid,
a lipopolysaccharide, a sterol, a lipid-linked molecule, and a
fatty acid.
4. The method of claim 1, wherein the lipid bilayer-associated
component is a bacterial endotoxin.
5. The method of claim 1, further comprising a label attached to
one or more of the lipid bilayer expanses.
6. The method of claim 5, wherein said label is attached to a
target membrane component.
7. The method of claim 5, wherein said label is attached to a
background membrane component.
8. The method of claim 5, wherein said label is selected from the
group consisting of a fluorophore, an electron spin resonance
label, a radioactive label, a semiconductor nanoparticle label, and
a metallic nanoparticle label.
9. The method of claim 1, wherein the test agent is an
antibody.
10. The method of claim 1, wherein the test agent is a small
molecule.
11. The method of claim 1, wherein the test agent is a protein.
12. The method of claim 1, wherein the test agent comprises a
surface of a cell, a vesicle, a phantom cell, a liposome, a giant
vesicle, a lipid-covered glass bead, or a component of any
thereof.
13. The method of claim 1, wherein the bulk aqueous phase further
comprises a second test agent and further comprising determining
whether said second test agent affects the interaction of the test
agent with the lipid bilayer-associated component.
14. A method for assaying an interaction between a test agent and a
lipid bilayer-associated component, comprising: providing a lipid
bilayer expanse comprising a lipid bilayer-associated component;
contacting said lipid bilayer expanse with a bulk aqueous phase
comprising the test agent that binds to said lipid
bilayer-associated component; and evaluating the acyl chain
mobility of said lipid bilayer expanse, wherein the acyl chain
mobility is affected when said test agent binds to the lipid
bilayer-associated component, and detecting binding of the test
agent to the lipid bilayer-associated component by correlating a
change in acyl chain mobility to binding.
15. The method of claim 14, wherein said evaluating acyl chain
mobility comprises using at least one of Fourier-transformed
infrared spectroscopy, sum frequency generation spectroscopy,
surface reflective spectroscopy, surface plasmon spectroscopy, and
imaging ellipsometry to determine acyl chain mobility.
16. The method of claim 14, wherein said lipid bilayer-associated
component is selected from the group consisting of a protein, a
nucleic acid, a glycolipid, a lipopolysaccharide, a sterol, a
lipid-linked molecule and a fatty acid.
17. The method of claim 14, wherein said lipid bilayer-associated
component is a bacterial endotoxin.
18. The method of claim 14, further comprising a label attached to
the lipid bilayer expanses.
19. The method of claim 18, wherein said label is attached to a
target membrane component.
20. The method of claim 18, wherein said label is attached to a
background membrane component.
21. The method of claim 18, wherein said label is selected from the
group consisting of a fluorophore, an electron spin resonance
label, a radioactive label, a semiconductor nanoparticle label, and
a metallic nanoparticle label.
22. The method of claim 14, wherein the test agent is an
antibody.
23. The method of claim 14, wherein the test agent is a small
molecule.
24. The method of claim 14, wherein the test agent is a
protein.
25. The method of claim 14, wherein the test agent comprises a
surface of a cell, a vesicle, a phantom cell, a liposome, a giant
vesicle, a lipid-covered glass bead, or a component of any
thereof.
26. The method of claim 14, wherein the bulk aqueous phase further
comprises a second test agent, and further comprising determining
whether said second test agent affects the interaction of the test
agent with the lipid bilayer-associated component.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to provisional U.S.
Application No. 60/410,173 filed Sep. 11, 2002, which is
incorporated herein by reference in its entirety.
FIELD OF THE INVENTION
[0002] The present invention relates in general to membrane-based
assays using fluid bilayers.
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
[0003] Not applicable.
BACKGROUND OF THE INVENTION
[0004] Over the last several years, a number of high-throughput
screening methods have been developed to facilitate the screening
of thousands, if not millions, of compounds for a desired activity
or activities. Such methods typically are based on detecting the
binding of a potentially effective compound to a receptor. While
these binding assays are effective at constraining the universe of
compounds which may have the desired activity, they typically are
not well-suited for evaluating this activity with any degree of
detail.
[0005] The biological activity of potentially active compounds
typically is evaluated using less efficient but more informative
"secondary screens" or assays that typically require a substantial
input of time by a trained technician or scientist. For evaluation
of candidate compounds affecting integral membrane proteins such as
receptors and ion channels, the amount of time required per
compound may be several hours or days if the assay includes effects
on electrophysiological activity. Evaluation of candidate compounds
affecting lipid bilayer properties also may be time consuming.
Accordingly, there is a need for a more efficient "secondary
screen" of compounds affecting the activity of membrane proteins,
other lipid bilayer-associated and integral components, including
the lipids in the bilayer themselves to identify those few
compounds that justify further detailed analysis.
BRIEF SUMMARY OF THE INVENTION
[0006] In one aspect, the present invention provides a method for
assaying an interaction between a test agent and a lipid-bilayer
and its associated and integral components that comprises
contacting said bilayer and its associated and integral components
with a bulk aqueous phase comprising a test agent and evaluating a
physical property of the lipid bilayer. In preferred embodiments,
the lipid bilayer expanse comprises part of a surface detector
array device.
[0007] In preferred embodiments, the physical property is selected
from the group consisting of membrane fluidity, acyl chain
mobility, membrane integrity, membrane appearance, membrane
continuity, membrane thickness, membrane bending modulus, and
membrane tension.
[0008] In other preferred embodiments, the lipid bilayer expanses
present on the device comprise a label. In certain embodiments, the
label is selected from the group consisting of a fluorophore, an
electron spin resonance label, a radioactive label, a semiconductor
nanoparticle label, and a metallic nanoparticle label.
[0009] In another preferred embodiment, the physical property is
membrane fluidity, which may be evaluated using a method selected
from the group consisting of fluorescence recovery after
photobleaching (FRAP), fluorescence anisotropy, fluorescence
correlation spectroscopy (FCS), fluorescence resonance energy
transfer (FRET), fluorescence resonance energy transfer microscopy
(FRET microscopy), electrophoresis, and electrical molecular force
microscopy.
[0010] In yet other preferred embodiments, the physical property is
membrane integrity. In preferred embodiments, membrane integrity is
evaluated by monitoring a parameter selected from the group
consisting of membrane resistance (or its reciprocal, membrane
conductance), membrane impedance, membrane current, and membrane
potential, or by using a method selected from the group consisting
of fluorescence recovery after photobleaching (FRAP), fluorescence
anisotropy, fluorescence correlation spectroscopy (FCS),
fluorescence resonance energy transfer (FRET), FRET microscopy,
Fourier-transformed infrared spectroscopy (FTIR), fluorescence
microscopy, electrophoresis, electrical molecular force microscopy,
reflection interference contrast microscopy, atomic force
microscopy (AFM), any other types of scanning probe microscopy,
such as lateral/frictional force microscopy and chemical force
microscopy, and quantitative image analysis of membrane
appearance.
[0011] In still other preferred embodiments, the physical property
is membrane continuity. In preferred embodiments, membrane
continuity is evaluated by monitoring a parameter selected from the
group consisting of membrane impedance, membrane resistance (or its
reciprocal, membrane conductance), membrane current, and membrane
potential or by using a method selected from the group consisting
of fluorescence recovery after photobleaching (FRAP), fluorescence
anisotropy, fluorescence correlation spectroscopy, (FCS),
fluorescence resonance energy transfer (FRET), fluorescence
resonance energy transfer microscopy (FRET microscopy),
electrophoresis, and electrical molecular force microscopy.
[0012] The test agent may be any substance whose interaction with a
lipid bilayer or a component thereof is desired to be tested.
Exemplary test agents include small molecules, polypeptides,
antibodies, and biomolecules. The test agent may be a cell surface,
a vesicle, a phantom cell, a cell-vesicle, a liposome (Sackmann,
Science, Vol 271, 1996, p 43-48), a giant vesicle (Wong and Groves,
JACS 123 (49) 12414-5), a lipid-covered glass bead, and/or a
component of any thereof, presented in the bulk aqueous phase. In
one variation, a second test agent may be employed to test its
effect on an interaction between the test agent and the lipid
bilayer; for example, a small molecule or antibody may be added to
the bulk aqueous phase to test its effect on an interaction between
a test agent and a component of the lipid bilayer.
[0013] In especially preferred embodiments, the agents tested may
be tested for their utility as antimicrobial compounds that
selectively interfere with and disrupt membrane structure, for
example, by selectively targeting microbial-specific membrane
targets in preference to orthologous human membrane targets. Such
agents can be identified by screening libraries of compounds,
including combinatorial libraries of biologicals such as polyenes,
cationic peptides, and lipopeptides, using a surface detector array
device.
BRIEF DESCRIPTION OF THE DRAWINGS
[0014] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawing(s) will be provided by the office
upon request and payment of the necessary fee.
[0015] FIG. 1 shows a portion of a surface detector array device
(SDAD) of the invention.
[0016] FIG. 2 shows the fluorescence intensity from two regions of
a surface detector array device, each containing a field-induced
concentration gradient of charged fluorescent reporter lipids.
[0017] FIG. 3 shows the structural portion of a device of the
invention suitable for use in a biosensor.
[0018] FIG. 4 depicts the result from a model drug discovery
experiment using a surface detector array device of the present
invention to illustrate the ability to array and physiologically
display different microbial-specific membrane targets and human
orthologous anti-targets. In this experiment the membrane targets
are exemplified by a glycolipid, ganglioside G.sub.M1, and the
fluorescently-labeled drug is cholera toxin subunit B, which
specifically binds ganglioside G.sub.M1.
[0019] FIGS. 5A-D depict the result of an experiment using a
surface detector array device of the present invention to
illustrate detection of cholera toxin binding to the ganglioside
G.sub.M1 by monitoring the fluidity of the lipid bilayer by FRAP.
FIGS. 5A and 5B respectively show control corral (minus cholera
toxin) at 0 minutes and at 5 minutes following photobleaching. Note
fluorescence recovery in FIG. 5B. FIGS. 5C and 5D respectively show
corral incubated with unlabeled cholera toxin at 0 minutes and at 5
minutes following photobleaching. Note bleached area remains in
5D.
[0020] FIG. 6A-D schematicize a model experiment using a surface
detector array device of the present invention to detect unlabeled
drug binding to its membrane target using electrophoresis to
monitor the fluidity of the lipid bilayer.
[0021] FIG. 7 is a top view of a well suitable for carrying out
electrophoresis based assays using the surface detector array
devices of the present invention.
[0022] FIG. 8. (A). Representative FRAP experiments on a pair of
500.times.500 .mu.m membrane corrals containing unlabeled
ganglioside GM1 (0.25% mole) with background lipids consisting of
DMPC (98.75% mole) and NBD-PG (1% mole). Experiments were performed
before and after exposure to CTB (1.40.times.10-7 M), as labeled.
The 0 min images depict the photobleached spots immediately after
exposure to bleaching light. Images taken 10 min later reveal the
extent of diffusive mixing. (B) Quantitative traces of fluorescence
intensity across the bleach spot at 0 and 10 min for a series of
FRAP experiments probing the change in mobility of each component
upon CTB binding, as labeled. The parameter, .DELTA.F, represents
the linearly integrated and normalized difference between before
and after fluorescence traces. A value of 0 indicates no diffusion
and a value of 1 indicates complete recovery.
[0023] FIG. 9 provides a schematic of Lipid Mobility Based
Detection. Without cholera toxin (top plane), unlabeled ganglioside
GM1 (membrane target) and a small amount of labeled lipid, NBD-PG,
diffuse freely within a DMPC bilayer. Unlabeled cholera toxin B
subunit pentamers (ligand) bind up ganglioside GM1, forming
structures studding the planar surface (bottom plane). These
interactions affect the overall state of the membrane and,
correspondingly, alter the mobility of the labeled lipids.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
I. Definitions
[0024] All terms, unless specifically defined below, are intended
to have their ordinary meanings as understood by those of skill in
the art. Claimed masses and volumes are intended to encompass
variations in the stated quantities compatible with the practice of
the invention. Such variations are contemplated to be within, e.g.,
about .+-.10-20 percent of the stated quantities. In case of
conflict between the specific definitions contained in this section
and the ordinary meanings as understood by those of skill in the
art, the definitions supplied below are to control.
[0025] The term "aqueous" refers to a water-based liquid medium
that is not deleterious to lipids.
[0026] A "receptor" is a macromolecule capable of specifically
interacting with a ligand molecule. In cells, receptors are
typically associated with lipid bilayer membranes, such as the
extracellular, Golgi or nuclear membranes. Receptors for
incorporation into expanses of lipids in vitro (e.g., supported
bilayers) may either be purified from cells, recombinantly
expressed, or, in the case of small receptors, chemically
synthesized.
[0027] A "ligand" is a molecule capable of specifically binding to
a receptor. Binding of the ligand to the receptor is typically
characterized by a high binding affinity, i.e.,
K.sub.a>10.sup.5, and can be detected either as a change in the
receptor's function (e.g., the opening of an ion channel associated
with or part of the receptor) or as a change in the immediate
environment of the receptor (e.g., detection of binding by surface
plasmon resonance). Ligands for incorporation into expanses of
lipids in vitro (e.g., supported bilayers) may either be purified
from cells, recombinantly expressed, or, in the case of small
ligands, chemically synthesized.
[0028] Binding is "specific" if it results from a molecular
interaction between a binding site on a receptor and a ligand,
rather than from "non-specific" sticking of the ligand to the
receptor. In cases where the ligand binds the receptor in a
reversible manner, specificity of binding can be confirmed by
competing off labeled ligand with an excess of unlabeled ligand
according to known methods. Non-specific interactions can be
minimized by including an excess of a protein (e.g., BSA) that does
not have binding sites for either the ligand or receptor.
[0029] A "fluid membrane" is a membrane having a native or
native-like bilayer structure, i.e., a bilayer organized with
opposing leaflets having hydrophobic tail groups on the interior of
the bilayer and hydrophilic headgroups on the exterior of the
bilayer. As one of ordinary skill will recognize, some "fluid
membranes" (i.e., those having high proportions of saturated lipids
and/or sterols) may not have appreciable fluidity, yet nonetheless
will be considered to be "fluid membranes" for purposes of the
present invention.
[0030] A "lipid bilayer vesicle" is a vesicle capable of fusing to
a bilayer-compatible surface region of the surface detector array
devices of the present invention to form a "fluid membrane." A
"lipid bilayer vesicle" may optionally contain, in addition to the
lipid components, other membrane components such as proteins,
glycoproteins, glycolipids, etc.
[0031] A "pinned lipid bilayer vesicle" refers to an absorbed but
un-ruptured or forced vesicle. The vesicle is pinned to the surface
but maintains its closed spherical structure.
[0032] "Assaying an interaction between a test agent and a
composition" means determining whether the test agent interacts
with the composition. "Assaying an interaction between a test agent
and a composition" may be done by detecting interaction of a test
agent to a composition using any method now known to one of skill
in the art, or later developed, and is intended to encompass
binding assays, such as direct binding and displacement assays,
electrophysiological assays, metabolic assays, etc.
[0033] A "lipid-bilayer associated component" refers to any
component comprising a lipid bilayer expanse including, e.g.,
lipids, glycolipids, sterols, lipid-linked (directly or indirectly,
e.g. by coupling directly to a lipid or by coupling to a binding
partner of a lipid-linked component) molecules, fatty acids,
proteins (both integral membrane proteins and extrinsic or
membrane-associated proteins), nucleic acids, etc.
[0034] A "target membrane component" refers to a "lipid-bilayer
associated component" that specifically binds a test agent.
[0035] A "background membrane component" refers to a "lipid-bilayer
associated component" other than a target membrane component.
[0036] A "transmembrane receptor" is an integral membrane protein
that, when present in a cell membrane, transduces a binding event
occurring on the extracellular side of the membrane into an
intracellular signal.
[0037] "T.sub.c temperature" refers to the gel-liquid crystal
transition temperature of a lipid or lipid mixture.
[0038] "Membrane bending modulus" refers to a physical parameter
that measures the stiffness of the membrane with respect to
bending.
[0039] "Membrane tension" refers to a physical parameter that
measures the tension in the membrane (i.e., force per distance).
Membrane tension also may be characterized by way of a parameter
that measures the stiffness of the membrane with respect to
stretching.
[0040] "Membrane integrity" refers generally to the degree to which
the overall structure of the membrane is intact. Membrane integrity
may be assayed by monitoring a parameter selected from the group
consisting of membrane impedance, membrane resistance (or its
reciprocal, membrane conductance), membrane current, and membrane
potential, or by using a method selected from the group consisting
of fluorescence recovery after photobleaching (FRAP), fluorescence
anisotropy, fluorescence correlation spectroscopy (FCS),
fluorescence resonance energy transfer (FRET), FRET microscopy,
Fourier-transformed infrared spectroscopy (FTIR), fluorescence
microscopy, electrophoresis, electrical molecular force microscopy,
reflection interference contrast microscopy, atomic force
microscopy (AFM), other types of scanning probe microscopy, such as
lateral/frictional force microscopy and chemical force microscopy,
and quantitative image analysis of membrane appearance. Signatures
of a fully intact membrane include long-range lateral fluidity of
the lipids with diffusion coefficients in the range of 1
micron.sup.2/sec (as determined by FRAP, e.g.). Because not all
membranes have sufficient fluidity to permit accurate measure of
diffusion coefficients other assays may sometimes need to be
employed to assess membrane integrity. AFM and other forms of
scanning probe microscopy can be used to reveal details about
surface topography of the membrane that can be used as a measure of
integrity. Intact membranes are flat and do not have major gaps or
bumps. FRET microscopy (Wong and Groves, 2001) also can be used to
characterize membrane topography.
[0041] "Membrane continuity" refers to the degree to which the
membrane bilayer forms a continuous two dimensional sheet within
which lipids diffuse freely. A large number of defects in the
membrane create obstacles that interrupt continuity and
connectivity of the fluid membrane. Molecules must navigate around
these defects to diffuse about the membrane. The existence of
defects that interrupt membrane continuity can have important
physiological consequences. Similarly, these defects affect
molecular mobility. Membrane continuity may be evaluated by
monitoring a parameter selected from the group consisting of
membrane impedance, membrane resistance (or its reciprocal,
membrane conductance), membrane current, and membrane potential, or
by using a method selected from the group consisting of
fluorescence recovery after photobleaching (FRAP), fluorescence
anisotropy, electrophoresis, and reflection interference contrast
microscopy.
[0042] "Members of a receptor protein family" refers to two or more
proteins that are related in structure and/or function within or
between organisms. Determining that proteins are "members of a
receptor protein family" may be done using computerized algorithms
known to persons of skill in the art to carry out, e.g., primary,
secondary, tertiary, or quaternary structure alignments.
Representative algorithms such as BLAST and VAST may be obtained
from the Computational Biology Branch, National Center for
Biotechnology Information, National Institutes of Health, 8600
Rockville Pike, Bethesda, Md. 20894 USA, and may be run directly
from the National Center for Biotechnology Information website,
www.ncbi.nlm.nih.gov.
[0043] "Electrical molecular force microscopy" refers to the use of
microscopy for the characterization of the electrophoretic mobility
and electric field induced concentration gradient of lipid membrane
components as described in, e.g., Groves and Boxer, 2002.
[0044] The term "antibody" as used herein includes antibodies
obtained from both polyclonal and monoclonal preparations, as well
as: hybrid (chimeric) antibody molecules (see, for example, Winter
et al. (1991) Nature 349:293-299; and U.S. Pat. No. 4,816,567);
F(ab')2 and F(ab) fragments; Fv molecules (noncovalent
heterodimers, see, for example, Inbar et al. (1972) Proc Natl Acad
Sci USA 69:2659-2662; and Ehrlich et al. (1980) Biochem
19:4091-4096); single-chain Fv molecules (sFv) (see, for example,
Huston et al. (1988) Proc Natl Acad Sci USA 85:5879-5883); dimeric
and trimeric antibody fragment constructs; minibodies (see, e.g.,
Pack et al. (1992) Biochem 31:1579-1584; Cumber et al. (1992) J
Immunology 149B: 120-126); humanized antibody molecules (see, for
example, Riechmann et al. (1988) Nature 332:323-327; Verhoeyan et
al. (1988) Science 239:1534-1536; and U.K. Patent Publication No.
GB 2,276,169, published 21 Sep. 1994); and, any functional
fragments obtained from such molecules, wherein such fragments
retain specific-binding properties of the parent antibody
molecule.
[0045] As used herein, the term "monoclonal antibody" refers to an
antibody composition having a homogeneous antibody population. The
term is not limited regarding the species or source of die
antibody, nor is it intended to be limited by the manner in which
it is made. Thus, the term encompasses antibodies obtained from
murine hybridomas, as well as human monoclonal antibodies obtained
using human hybridomas or from murine hybridomas made from mice
expression human immunoglobulin chain genes or portions thereof.
See, e.g., Cote, et al. Monoclonal Antibodies and Cancer Therapy,
Alan R. Liss, 1985, p. 77.
II. Surface Detector Array Device
[0046] FIG. 1 is a perspective view of a portion of a surface
detector array device (SDAD) 20 in accordance with the invention.
The device is fabricated from a substrate 22, such as an oxidized
silicon or fused silica wafer. The dimensions of the substrate are
typically between about 0.1 cm to about 10 cm per side and about
0.01 mm to about 1 cm in thickness.
[0047] The substrate surface contains a plurality of distinct
bilayer-compatible surface regions 24 separated by one or more
bilayer barrier regions 26. The bilayer barrier region(s) 26 are
preferably formed of a material 28 different from the material 22
forming the bilayer-compatible surface regions 24.
[0048] A lipid bilayer expanse 30 is carried on each of the
bilayer-compatible surface regions 24. Interposed between each
bilayer-compatible surface region 24 and corresponding lipid
bilayer expanse 30 is an aqueous film 32 that is between about 5
.ANG. and 15 .ANG. (typically about 10 .ANG.) in thickness. In some
configurations, separation of up to 1 micron can be achieved (Wong
and Groves, 2001, incorporated herein by reference). Covering the
substrate surface and lipid expanses is a bulk aqueous phase
34.
[0049] The bilayer barrier regions may be depressed, flush, or
elevated (as shown at 26 in FIG. 1), with respect to the
bilayer-compatible surface 24. In embodiments having elevated
barriers, the height of the barrier may range from tens of
Angstroms to several micrometers or more. The width of the barriers
is typically between about 100 nm and about 250 .mu.m. Preferably,
the width is between about 1 .mu.m and 100 .mu.m.
[0050] According to results of experiments performed in support of
the invention, the lipid barrier regions do not function simply by
mechanical or physical separation of adjacent lipid bilayer
regions. Rather, the experiments indicate that the characteristics
which allow a surface to act as a bilayer barrier region are
chemical/electrostatic properties intrinsic to the material making
up the surface. Examples of such chemical/electrostatic properties
include hydrophobicity, dielectric permeability, conductivity, and
surface charge density.
[0051] Similarly, the degree of "bilayer-compatibility" of a
selected surface is a function of its intrinsic material properties
rather than its shape. The interactions between membranes and
surfaces involve electrostatic and hydration forces as well as
attractive contributions from long-range van der Waals forces. In a
suitable bilayer-compatible surface, an energetic minimum traps the
bilayer membrane between about 5 .ANG. and 15 .ANG. (typically
about 1.degree. A) away from the supporting surface, separated from
the supporting surface by an aqueous film of corresponding
thickness. Bilayer-compatible surfaces typically are hydrophilic.
Details regarding the selection and testing of materials for use as
bilayer-compatible surfaces and bilayer barrier regions are
provided in U.S. Pat. No. 6,228,326, incorporated herein by
reference.
[0052] Exemplary materials having properties making them suitable
for lipid bilayer barriers include certain polymers (e.g.,
photoresist) and various metals (e.g., gold) and minerals (e.g.,
aluminum oxide). An advantage of photoresist is that it is
relatively easy to pattern with a photomask and is nonconductive.
Aluminum oxide has the advantage of being both nonconductive and
reusable, withstanding most cleaning procedures.
[0053] Exemplary materials having properties making them suitable
for bilayer-compatible surfaces include various glasses, silicon
oxides, including oxidized silicon (SiO.sub.2), MgF.sub.2,
CaF.sub.2, mica, and various polymer films, such as thin
polyacrylamide or dextran films (see, e.g., Elender, et al., 1996;
Khuner, et al., 1994), both incorporated herein by reference). Both
types of polymer films form a suitable bilayer-compatible surface
that is hydrated to provide a film of aqueous between the polymer
film and the supported bilayer membrane.
[0054] To generate a substrate surface that is
"bilayer-compatible", the surface typically is cleaned and/or
treated to remove surface impurities (dirt, oils, etc.). Suitable
treatments are discussed below with respect to the making or
construction of a device of the invention.
[0055] The supported bilayer itself is a self-assembling,
two-dimensional fluid system, typically consisting of two opposed
leaflets of vesicle-forming lipid molecules. However, it can be
constructed as described below from any suitable membrane-forming
amphiphile, including proteins and nonlipids.
[0056] Most vesicle-forming lipids are long-chain carboxylic acids,
such as glycerides, having the hydroxyl groups of the glycerol
esterified with (i) fatty acid chain(s), and (ii) a charged or
polar moiety, such as a phosphate-ester group. The vesicle-forming
lipids are preferably ones having two hydrocarbon chains, typically
acyl chains, and a polar head group. Long-chain carboxylic acids
with a phosphate group, or phospholipids, are particularly
well-suited for use with the present invention. There are a variety
of synthetic vesicle-forming lipids and naturally-occurring
vesicle-forming lipids, including the phospholipids, such as
phosphatidylcholine (PC), phosphatidylethanolamine (PE),
phosphatidylserine (PS), phosphatidic acid, phosphatidylinositol
(PI), phosphatidylglycerol (PG), and sphingomyelin, where the two
hydrocarbon chains are typically between about 14-22 carbon atoms
in length, and have varying degrees of unsaturation. The
above-described lipids and phospholipids whose acyl chains have
varying degrees of saturation can be obtained commercially or
prepared according to published methods. Other suitable lipids
include glycolipids and sterols such as cholesterol.
[0057] Preferred diacyl-chain lipids for use in the present
invention include diacyl glycerol, phosphatidyl ethanolamine (PE)
and phosphatidylglycerol (PG). These lipids are preferred for use
as the vesicle-forming lipid, the major liposome component, and for
use in the derivatized lipid described below. All of these
phospholipids and others are available from specialized suppliers
of phospholipids (e.g., Avanti Polar Lipids, Inc., Alabaster, Ala.)
as well as from general chemical suppliers, such as Sigma Chemical
Co. (St. Louis, Mo.).
[0058] The aqueous film and bulk aqueous phase may be any suitable
aqueous solution, such as a buffered saline solution (e.g., PBS).
The bulk solution can be readily changed (taking care, of course,
to keep the supported bilayer submerged at all times) by, e.g.,
flow-through rinsing with a solution having a different
composition.
[0059] As described above, FIG. 1 shows a support grid
microfabricated from a wafer of a material that forms the
bilayer-compatible surfaces of the device. A device may also be
microfabricated, however, from a wafer of a material that forms the
bilayer-barrier surface regions of the device. One embodiment of
such a device is shown in FIG. 3. Here, the structural portion 50
of a device of the invention is produced by microfabricating a
wafer of a bilayer barrier material 52 (e.g., aluminum oxide) to
contain regions, such as region 54, consisting of a
bilayer-compatible material, where each region corresponds to one
of the plurality of distinct bilayer-compatible surface regions,
such as region 56. In one embodiment, the regions 54 are
electrically-conductive and are connected to leads 58 which can be
used to record changes in, e.g., the membrane potential at the
bilayer surface, capacitative transients, or membrane current. An
example of an electrically-conductive bilayer-compatible material
is a metal, such as gold, coated with a thin film of silicon oxide
or polymer material to make the surface bilayer-compatible. The
thin film of silicon oxide, while not an electrical conductor, can
effectively pass capacitative current. Another suitable substrate
is indium tin oxide (ITO) because of its conductivity and its
ability to support direct membrane deposition (Sackmann and Tanaka,
2000; Hillebrandt, et al., 1999; Salafsky, Groves, and Boxer, 1996,
incorporated by reference).
[0060] Alternatively or in addition, electrodes having a
bilayer-compatible surface may be generated from standard doped
(e.g., boron-doped) silicon wafers. A layer of silicon oxide may be
formed on such wafer substrates to provide a bilayer-compatible
surface, under which resides a semi-conductor (doped silicon)
electrode. The semi-conductor electrode can, of course, be
interfaced with any of a variety of other elements, e.g., semi
conductor elements in the substrate itself or in a separate chip,
as desired, to facilitate or enhance the processing of information
from the patch of bilayer membrane corresponding to that
electrode.
[0061] A number of different devices have been produced in
accordance with the invention. They include the following (i) a
device containing a 1 cm.sup.2 array of 2500 identical 200 .mu.m
square corrals or regions, (ii) a device containing a 1 cm.sup.2
array of 10,000 identical 100 .mu.m square regions, (iii) a device
containing a 1 cm.sup.2 array of about 37,000 identical 50 .mu.m
square regions separated by 2 .mu.m barriers of photoresist, and
(iv) a device containing a 1 cm.sup.2 array of about 2.8 million 5
.mu.m square corrals or regions separated by 1 .mu.m-wide barriers
of photoresist.
[0062] Exemplary embodiments of the invention include devices where
the bilayer lipid expanses contain different biomolecules, such as
receptor protein molecules, ligand protein molecules other protein
molecules, lipids, glycolipids, including lipopolysaccharides and
sphingolipids, fatty acids, for example, mycolic acid or sterols,
such as ergosterol and cholesterol. Such devices are particularly
useful in biosensors, described more fully in U.S. Pat. No.
6,228,326, and in U.S. application Ser. No. 10/200,682, filed Jul.
22, 2002 (attorney docket number 23604-7001), both of which are
incorporated herein by reference, and are made as described below
by fusing proteoliposomes to the bilayer-compatible surface.
[0063] In addition to incorporation of receptors or ion channels
into the bilayer membrane, the bilayer may be derivatized with any
of a number of groups or compounds to create a surface having the
desired properties. For example, the liposomes may contain a ligand
bound to the surface of the lipid by attachment to surface lipid
components. Generally, such a ligand is coupled to the polar head
group of a vesicle-forming lipid. Exemplary methods of achieving
such coupling are described in U.S. Pat. No. 6,228,326.
III. Construction of a Surface Detector Array Device with
Independently-Addressable Lipid Bilayer Regions
[0064] Surface detector devices used in the present invention may
be conveniently produced using a combination of microfabrication
and lipid vesicle technologies, e.g., as described in Example 1 of
U.S. Pat. No. 6,228,326.
[0065] The surface detector array devices used in the present
invention are typically fabricated by patterning a substrate to
produce a substrate surface having a plurality of distinct
bilayer-compatible surface regions separated by one or more bilayer
barrier regions. Electrodes may be fabricated into the device using
any of a number of different techniques that are available for
applying thin metal coatings to a substrate in a desired pattern.
Exemplary techniques are reviewed in, e.g., Krutenat, 1986; and in
Wolf and Tauber, 1986, both incorporated herein by reference. After
the patterned support grid is made, it is cleaned and/or treated to
strip or etch off any impurities or contaminants present on the
substrate surface which might otherwise inhibit the formation of a
lipid bilayer adjacent the surface. Following the
wash/etching/treatment step, the grid is placed in a chamber and a
suspension of vesicles or liposomes formed of selected lipid(s) and
(optionally) containing selected proteins or other biomolecules is
contacted with each bilayer-compatible surface region. Vesicles in
the suspension generally fuse with the bilayer-compatible surface
region within a minute or less to form a supported bilayer membrane
(Xia, et al., 1996; Groves, et al., 1996, both of which are
incorporated herein by reference). Detailed methods of fabricating
and using surface detector array devices of the present invention
are contained in U.S. Pat. No. 6,228,326, and in U.S. application
Ser. No. 10/200,682, filed Jul. 22, 2002 (attorney docket number
23604-7001), both of which are incorporated herein by
reference.
IV. Binding Detection
[0066] Binding events to lipid bilayer membranes and their
associated and integral components may be detected using bilayer
membranes in various formats, including supported lipid bilayers,
black lipid membranes, asymmetric and symmetric lipid bilayers,
lipid bilayer vesicles, membrane-coated microbeads and vesicles,
pinned lipid bilayer vesicles, and lipid bilayer coated capillary
walls. In accordance with the present invention, binding events are
detected through their effects on one or more physical properties
of the lipid bilayer. These properties include, by way of example,
but not limitation, membrane fluidity, acyl chain mobility,
membrane integrity, membrane appearance, membrane continuity,
membrane thickness, membrane bending modulus, and membrane
tension.
[0067] Binding events may be detected using imaging techniques,
some of which rely on the use of a label, such as a fluorophore, an
electron spin resonance label, a radioactive label, a semiconductor
nanoparticle label, or a metallic nanoparticle label attached to or
incorporated within a membrane or membrane-associated component.
See, for example Taton, et al., 2001; Hu., et al., 2001
(incorporated by reference). Interaction of a second membrane with
the first membrane can also reveal details of membrane structure
and organization. See Wong, and Groves, 2001 (incorporated by
reference). In some embodiments, the membrane target component such
as, e.g., a target lipid or other membrane component may be
labeled, while in other embodiments, a background lipid or other
membrane component may be labeled. In this latter embodiment,
binding of an agent to the target is read out indirectly by
monitoring the effect of binding on the behavior of the background
lipid or other membrane component. This indirect read out is
possible because effects of binding on the target component are
transmitted to the background lipid or other membrane components.
For example, binding-induced alterations in the fluidity of a
target component (such as is observed when cholera toxin binds to
the ganglioside G.sub.M1, as described, infra) can affect the
fluidity of lipid molecules in the neighborhood of the ganglioside.
If those background lipid molecules are labeled, then alterations
in their behavior can be used to monitor binding of cholera toxin
to G.sub.M1.
[0068] Membrane binding events may be detected using, by way of
example but not limitation, measurements of membrane fluidity by
way of, e.g., fluorescence recovery after photobleaching (FRAP) as
described in e.g., Tamm and Kalb, 1993, incorporated herein by
reference, fluorescence anisotropy, as described in, e.g.,
Lackowicz, 1999, incorporated herein by reference, fluorescence
correlation spectroscopy (FCS), as described in, e.g., Hess, et
al., 2002, incorporated herein by reference, fluorescence resonance
energy transfer (FRET), as described in, e.g., Clegg, 1996,
incorporated herein by reference, fluorescence resonance energy
transfer microscopy (FRET microscopy), electrophoresis, and
electrical molecular force microscopy, as described in, e.g.,
Groves and Boxer, 2002, incorporated herein by reference.
[0069] Acyl chain mobility may be evaluated using, e.g.,
electron-spin labeled lipids as described in, e.g., Yin and Hyde,
1989, incorporated herein by reference, or by FTIR, as described
in, e.g., Griffiths, et al., 1986, incorporated herein by
reference, sum frequency generation spectroscopy, or surface
reflective spectroscopy as described in, e.g., Kim, et al., 2002,
incorporated by reference.
[0070] Membrane integrity may be evaluated by measuring, e.g., a
parameter selected from the group consisting of membrane impedance
or resistance (or its reciprocal, membrane conductance) as
described in, e.g. Sackmann and Tanaka, 2000, Hillebrandt, et al.,
1999, or Salafsky, Groves and Boxer, 1996, incorporated herein by
reference, membrane current, as described in, e.g., Sackmann and
Tanaka, 2000, Hillebrandt, et al., 1999, or Salafsky, Groves and
Boxer, 1996, membrane capacitance or capacitative current, as
described in, e.g., Sackmann and Tanaka, 2000, or in Cornell, et
al., 1997, incorporated herein by reference and membrane potential,
as described in, e.g., Sackmann and Tanaka, 2000, or by using a
method selected from the group consisting of fluorescence recovery
after photobleaching (FRAP) as described in e.g., Tamm and Kalb,
1993, incorporated herein by reference, fluorescence anisotropy, as
described in, e.g., Lackowicz, Principles of Fluorescence
Spectroscopy, Kluwer Academic/Plenum, New York, 1999, incorporated
herein by reference, fluorescence correlation spectroscopy (FCS),
as described in, e.g., Hess, et al., 2002, incorporated herein by
reference, fluorescence resonance energy transfer (FRET), as
described in, e.g., Clegg, 1996, incorporated herein by reference,
FRET microscopy, as described in, e.g., Wong and Groves, 2001,
Fourier-transformed infrared spectroscopy (FTIR), as described in,
e.g., Griffiths, et al., 1986, incorporated herein by reference,
fluorescence microscopy, electrophoresis, electrical molecular
force microscopy, as described in, e.g., Groves and Boxer, 2002,
incorporated herein by reference, reflection interference contrast
microscopy, as described in, e.g., Hillner, et al., 1995,
incorporated herein by reference, atomic force microscopy (AFM), as
described in, e.g., Binnig, et al., 1986, incorporated herein by
reference, any other types of scanning probe microscopy, such as
lateral/frictional force microscopy, as described in, e.g.,
Colchero, et al., 1992, incorporated herein by reference, chemical
force microscopy, as described in, e.g., Frisbie, et al. 1994,
incorporated herein by reference, and by quantitative image
analysis of membrane appearance.
[0071] Membrane continuity may be evaluated by monitoring a
parameter selected from the group consisting of membrane impedance,
membrane resistance (or its reciprocal, membrane conductance), as
described in, e.g., Sackmann and Tanaka, 2000, Hillebrandt, et al.,
1999, or Salafsky, Groves and Boxer, 1996, each incorporated herein
by reference, membrane current, as described in, e.g. Sackmann and
Tanaka, 2000, Hillebrandt, et al., 1999, or Salafsky, Groves and
Boxer, 1996, membrane potential as described in, e.g., Sackmann and
Tanaka, 2000, and membrane fluidity as described, supra, or by
using a method selected from the group consisting of fluorescence
recovery after photobleaching (FRAP) as described in e.g., Tamm and
Kalb, 1993, incorporated herein by reference, fluorescence
anisotropy, as described in, e.g., Lackowicz, Principles of
Fluorescence Spectroscopy, Kluwer Academic/Plenum, New York, 1999,
incorporated herein by reference, fluorescence correlation
spectroscopy (FCS), as described in, e.g., Hess, et al, 2002,
incorporated herein by reference, fluorescence resonance energy
transfer (FRET), as described in, e.g., Clegg, 1996, incorporated
herein by reference, FRET microscopy, as described in, e.g., Wong
and Groves, 2001, electrophoresis, and electrical molecular force
microscopy, as described in, e.g., Groves and Boxer, 2002,
incorporated herein by reference.
[0072] Membrane appearance may be evaluated using, e.g., reflection
interference contrast microscopy, as described in, e.g., Hillner,
et al., 1995, incorporated herein by reference, electrical
molecular force microscopy, as described in, e.g., Groves and
Boxer, 2002, incorporated herein by reference, atomic force
microscopy (AFM), as described in, e.g., Binnig, et al., 1986
incorporated herein by reference, or any other types of scanning
probe microscopy, such as lateral/frictional force microscopy, as
described in, e.g., Colchero, et al., 1992, incorporated herein by
reference and chemical force microscopy, as described in, e.g.,
Frisbie, et al., 1994, incorporated herein by reference. Membrane
appearance differs from, e.g., membrane integrity or membrane
continuity in that appearance refers to a static evaluation of the
membrane, akin to a snapshot, and so does not assure the integrity
or continuity of the membrane after the static evaluation has been
made.
[0073] Membrane thickness may be evaluated through measurements of,
e.g., membrane capacitance, as described in, e.g., Sackmann and
Tanaka, 2000, or in Cornell, et al., 1997, incorporated herein by
reference, or by using atomic force microscopy (AFM), as described
in, e.g., Binnig, et al., 1986, incorporated herein by
reference.
[0074] Membrane bending modulus may be evaluated using, e.g.,
techniques taught by Lipowsky and Sackmann, 1995, incorporated
herein by reference.
[0075] Membrane tension may be evaluated using, e.g., techniques
taught by Lipowsky and Sackmann, 1995, incorporated herein by
reference.
[0076] Many of the techniques used in conjunction with the present
invention for imaging or otherwise determining aspects of lipid
bilayer membrane structures in various formats, including supported
lipid bilayers, black lipid membranes, asymmetric and symmetric
lipid bilayers, lipid bilayer vesicles, pinned lipid bilayer
vesicles, and lipid bilayer coated capillary walls, may be carried
out without the use of exogenous labels. These include the
techniques of reflection interference contrast microscopy,
electrical molecular force microscopy, Atomic Force Microscopy
(AFM) or any other types of scanning probe microscopy, such as
lateral force or chemical force, Fourier-transformed infrared
spectroscopy (FTIR), microcalorimetry, measures of membrane
composition by mass spectrometry (MS), surface plasmon resonance,
measurements of membrane bending modulus, measures of membrane
tension and its associated constant, to name a few. Such techniques
are well-known to those of skill in the art and are described in,
e.g., Safran, 1994; Hess, et al. 2002; and Lipowsky and Sackmann,
1995.
[0077] Electrical measurements can be performed on lipid bilayer
membrane structures of various formats, including supported lipid
bilayers, black lipid membranes, asymmetric and symmetric lipid
bilayers to detect membrane binding and disrupting events. Besides
membrane impedance, membrane resistance, or its reciprocal,
membrane conductance, (see, e.g., Sackmann and Tanaka, 2000;
Hillebrandt, et al., 1999; and Salafsky, Groves, and Boxer, 1996,
incorporated herein by reference) two other parameters of bilayers
can be used to get further information on the action of potential
membrane-active drugs or agents, namely membrane capacitance (see,
e.g., Sackmann and Tanaka, 2000; and Cornell, et al., 1997,
incorporated herein by reference) and innermembrane potential
difference (see, e.g., Sackmann and Tanaka, 2000, and Cornell, et
al., 1997, incorporated herein by reference). The determination of
membrane capacitance yields information on area, thickness and
composition of the bilayer. The intrinsic membrane potential is
composed of the surface and the innermembrane potential. Changes in
the membrane conductance and capacitance and the innermembrane
potential indicate binding to lipid bilayer membrane structures
including the lipid components or associated or intrinsic
components, resulting in an alteration of the permeability of the
bilayer to one or more ionic species. These electrical measurements
may be carried out on supported membranes using porous substrates
as well as conductive membrane-supporting substrates such as
indium-tin-oxide (ITO).
[0078] The following examples illustrate but in no way are intended
to limit the present invention.
[0079] Materials and Methods
[0080] Unless otherwise indicated, chemicals were purchased from
Sigma (St. Louis, Mo.) or United States Biochemical (Cleveland,
Ohio).
[0081] A. Buffers
[0082] Standard Buffer [0083] 10 mM Tris [0084] 100 mM NaCl (pH
8.0)
[0085] Phosphate-Buffered Saline (PBS)
[0086] 10.times. stock solution, 1 liter:
[0087] 80 g NaCl [0088] 2 g KCl [0089] 11.5 g
Na.sub.2HPO.sub.4.7H.sub.2O [0090] 2 g KH.sub.2PO.sub.4
[0091] Working Solution of PBS, pH 7.3: [0092] 137 mM NaCl [0093]
2.7 MM KCl [0094] 4.3 mM Na.sub.2HPO.sub.4.7H.sub.2O [0095] 1.4 mM
KH.sub.2PO.sub.4
[0096] B. Lipids and Labels
[0097] L-.alpha. phosphatidylcholine from egg (egg-PC) was obtained
from Avanti Polar Lipids (Alabaster, Ala.). The fluorescent probe N
(Texas Red
sulfonyl)-1,2-dihexadecanoyl-sn-glycero-3phosphoethanolamine,
triethylammonium salt (Texas Red DHPE) was obtained from Molecular
Probes (Eugene, Oreg.).
[0098] C. Preparation of Phospholipid Vesicles
[0099] Small unilamellar vesicles (SUVs) were prepared by following
the protocol outlined in Barenholz, et al., 1977 (incorporated by
reference) using egg L-.alpha. phosphatidylcholine (Avanti). The
phosphatidylcholine was mixed with 1 mole % Texas red DHPE in
HPLC-grade chloroform (SigmaAldrich) and dried in a vacuum
desiccator overnight. The dried lipids were resuspended to about 6
mg/ml in standard buffer that had been filtered through Rainin
Nylon-66 0.45 .mu.m filters using a Sibata filter unit. The
suspension was sonicated to clarity with a Branson ultrasonicator
under flowing Ar on ice for 3 minute periods separated by 1 minute
cooling periods (Martin, 1990 (incorporated by reference)).
[0100] The sample then was spun for 30 minutes at 100,000.times.g
to remove Ti particles shed from the sonicator tip, and the
supernatant was spun for 4 hours at 166,000.times.g to obtain the
SUVs. The SUVs were stored at 4.degree. C. under N.sub.2 or Ar in
the dark and were used within three weeks. The lipid concentration
in these samples was determined from the Texas Red probe absorption
at 590 nm (.xi.=100,000 M.sup.-1cm.sup.-1; Haugland, 1992) assuming
that the probe concentration in the vesicles is 1 mole % as
prepared. Yields (mg SUV lipid/mg initial lipid) are calculated
from this concentration and are equal to those reported by
Barenholz, et al., 1977.
[0101] D. Membrane Electrophoresis
[0102] For the electrophoretic studies, the supported membrane in
PBS was diluted to 1 mM total ionic strength. This was then
assembled, under buffer, into a sandwich with another coverslip.
The electrophoresis cell consisted of two 0.01'' diameter platinum
wire electrodes in solution-filled wells of a Teflon trough. The
coverslip sandwich was arranged to form a bridge between the two
electrode wells. Electrical connection was achieved through the
solution in the cover slip sandwich. Fields up to 60 V/cm were
applied with a standard power supply. Currents were monitored with
a Keithley picoammeter (Cleveland, Ohio) and typically were around
3 .mu.A for a single 18 mm square coverslip sandwich at 15 V/cm.
This corresponds to a total power dissipation of 9.times.10.sup.-5
W which should produce a negligible amount of Joule heating.
Example 1
Membrane Electrophoresis in a Surface Detector Device
[0103] A surface detector device with 200 .mu.m square corrals was
prepared as described above and in Example 1 of U.S. Pat. No.
6,228,326 using L-.alpha.-phosphatidylcholine (PC) molecules doped
with 1 mole percent of the fluorescently labeled lipid, Texas Red
DHPE (Molecular Probes, Eugene, Oreg.).
[0104] Briefly, membranes were formed by contacting the patterned
surface of the wafer support grids with a suspension, prepared as
described above, containing .about.25 nm diameter unilamellar
vesicles consisting primarily of molecules doped with 1 mole
percent of the fluorescently labeled lipid, Texas Red DHPE. Excess
vesicles were rinsed away while maintaining the membrane under the
bulk aqueous solution at all times.
[0105] The fluidity of the supported bilayers on the
bilayer-compatible surface regions was demonstrated by
electrophoretic redistribution of charged membrane components.
Electrophoresis was carried out using the technique described in
Materials and Methods section D, above. An electric field of 15
V/cm was applied parallel to the plane of the lipid bilayer
membrane. Upon application of the field, the charged molecules
(labeled DHPE) drifted in the plane of the bilayer, whereas the
neutral PC molecules, forming the bulk of the membrane, were
unaffected by the field. Application of the field for 25 minutes
resulted in a steady-state, electric field-induced concentration
profile (Groves and Boxer, 1995 (incorporated by reference)) of the
negatively-charged fluorescent probe.
[0106] A quantitative description of the field-induced
concentration gradient is depicted in FIG. 2, which shows
quantitative traces of fluorescence intensity calculated from
videomicrographs of steady-state concentration gradients of the
fluorescent probe lipid (Texas Red DHPE) in two 200 .mu.m
microfabricated corrals. The concentration gradients in this
experiment adopted an exponential profile. The image from which the
fluorescence intensity traces were calculated was taken with a low
light level video camera which had been adjusted for linear imaging
of fluorescence intensity.
[0107] The field-induced concentration gradients were fully
reversible, taking approximately the same amount of time to
dissipate as they took to form at 15 V/cm. The profiles could be
switched by reversing the polarity of the field repeatedly without
any apparent effect on the membrane or the bilayer-barrier regions,
or barriers. The field-induced concentration profiles described
above can be used to study molecular size, clustering, non-ideal
mixing, and ligand binding.
Example 2
Screening Membrane Targets
[0108] The purpose of this experiment is to illustrate the
feasibility of utilizing the surface detector array device, or
"MembraneChip.TM.," for drug discovery, by utilizing the specific
binding of the cholera toxin B subunits to the
fluorescently-labeled glycolipid, ganglioside G.sub.M1. Any other
membrane associated or integral components, such as other
glycolipids, fatty acids, and sterols, can also be displayed on
MembraneChips.TM. as membrane targets.
[0109] Cholera toxin is a membrane-targeting hexamer involving two
different types of subunits, in an AB5 configuration. The toxin is
secreted by Vibrio cholerae, a pathogen that accounts for over one
million deaths, annually. The A subunit disrupts G-protein
signaling, while the nontoxic B subunits are responsible for
binding to cell surfaces. Each B subunit binds specifically to a
pentasaccharide chain, that the ganglioside G.sub.M1 displays on
its head region. G.sub.M1 is a naturally-occurring
carbohydrate-rich sphingolipid found in the membranes of intestinal
mucosal cells. In this way, cholera toxin gains entry into human
intestinal cells to cause potentially lethal diarrhea.
[0110] Cholera Toxin subunit B, Alexa Fluor 594 was purchased from
Molecular Probes (Eugene, Oreg.), and was received as a 500 .mu.g
lyophilized powder. A stock solution of 2.0 mg/ml was made and
aliquots of 10 .mu.l were stored in the -20.degree. C. freezer in a
light-safe box.
[0111] The G.sub.M1 (from sheep brain) came from Avanti Polar
Lipids (Alabaster, Ala.) in a mixture of 65:25:4
chloroform:methanol:water. Two ampoules contained 0.5 ml each, with
2.5 mg in each (for a concentration of 5 mg/ml). L-.alpha.
phosphatidylcholine from egg (egg-PC) were obtained from Avanti
Polar Lipids (Alabaster, Ala.). The fluorescent probe N (Texas Red
sulfonyl)-1,2-dihexadecanoyl-sn-glycero-3phosphoethanolamine,
triethylammonium salt (Texas Red DHPE) was obtained from Molecular
Probes (Eugene, Oreg.).
[0112] Vesicle preparations were made according to the methods
outlined above. Varying amounts of the ganglioside were tested with
the fluorescently-labeled cholera toxin to determine the percentage
of G.sub.M1 to be included in the membrane for cholera toxin
binding assays. It was determined through fluorescence microscopy
that 1 mole percent is an acceptable concentration. This result was
confirmed on a MembraneChip.TM. surface detector device. See
Example 2 (supra) and FIG. 4. Spreading solutions were created by
adding 12.5 .mu.l of the vesicle preparation to 12.5 .mu.l PBS
buffer.
[0113] A surface detector device (i.e., MembraneChip.TM.) was
constructed according to the automated methods described in Example
6 of U.S. application Ser. No. 10/200,682, filed Jul. 22, 2002
(attorney docket number 23604-7001). In a four by four array having
500 micron.sup.2 features (i.e. corrals) all but one of the corrals
was arrayed with a solution containing 99 mole percent egg
phosphatidylcholine with 1 mole percent NBD-phosphatidylglycerol.
The last corral (third column, third row, origin at top left
corner) was arrayed with 98 mole percent egg phosphatidylcholine, 1
mole percent NBD-phosphatidylglycerol and 1 mole percent unlabeled
G.sub.M1. When observed under a fluorescence microscope (Nikon
Instruments, Inc., Nikon Eclipse E400, Melville, N.Y.) outfitted
with the appropriate FITC filter set (Nikon Instruments, Inc.,
96106807B-2A, Melville, N.Y.), the chip appeared uniformly green
(data not shown).
[0114] Cholera toxin specifically binds to the ganglioside
G.sub.M1. The MembraneChip.TM. was able to detect this specific
interaction. The MembraneChip.TM. was incubated with 1 ml of 2
.mu.g/ml Texas Red-labeled cholera toxin (Molecular Probes, Eugene,
Oreg.) in phosphate buffered saline for 1 hour at room temperature.
Following incubation, the MembraneChip.TM. % was washed by removing
the cholera toxin-containing solution, and 1 ml of phosphate
buffered saline at room temperature was added. The wash step was
repeated 4 more times. Only the corral containing the 1 mole
percent G.sub.M1 bound cholera toxin. When imaged with a
fluorescence microscope, the G.sub.M1-containing corral 40 appeared
red, while the other corrals, lacking G.sub.M1, do not bind any
cholera toxin and so remained green. These results, shown in FIG.
4, illustrate that specific binding of cholera toxin to G.sub.M1
can be detected using the MembraneChip.TM. surface detector
devices.
Example 3
Detection of Binding by Alteration in Membrane Fluidity
[0115] Binding assays, such as those described above for cholera
toxin, often require use of a labeled ligand to facilitate binding
detection. Use of labeled ligands can create additional bottlenecks
in screening processes, increase the expense of assays that require
their use, or, depending on the specific label and its attachment
point, alter ligand binding properties. Here we describe the use of
membrane fluidity measurements to assay binding interactions. We
illustrate that cholera toxin binding to membranes presenting
G.sub.M1 decreases the lateral mobility of gangliosides within the
membrane.
[0116] Materials and Methods
[0117] Cholera Toxin B subunit labeled with Alexa Fluor 594 was
purchased from Molecular Probes (Eugene, Oreg.), and was received
as 500 .mu.g lyophilized B subunits. 0.25 ml water was added to
create a 2.0 mg/ml solution, and 10 .mu.l aliquots were partitioned
and stored in a -20.degree. C. freezer in a light-safe box.
[0118] Unlabeled Cholera Toxin B subunit was purchased from Sigma
(St. Louis, Mo.), and 0.25 ml water was added to the 500 .mu.g
lyophilized powder to create a stock solution of 2.0 mg/ml. 10
.mu.l aliquots were made, and stored in a -20.degree. C. freezer in
a light-safe box.
[0119] G.sub.M1 (from sheep brain) was purchased from Avanti Polar
Lipids (Alabaster, Ala.) in a mixture of 65:25:4
chloroform:methanol:water. Two ampoules contained 0.5 ml each, with
2.5 mg in each (for a concentration of 5 mg/ml). BODIPY FL
C5-ganglioside G.sub.M1 was obtained from Molecular Probes (Eugene,
Oreg.). L-.alpha. phosphatidylcholine from egg (egg-PC) were
obtained from Avanti Polar Lipids (Alabaster, Ala.). The
fluorescent probe N (Texas Red
sulfonyl)-1,2-dihexadecanoyl-sn-glycero-3phosphoethanolamine,
triethylammonium salt (Texas Red DHPE) was obtained from Molecular
Probes (Eugene, Oreg.).
[0120] Vesicle preparations were made, according to the methods
outlined above. Varying amounts of the ganglioside were tested with
the fluorescently-labeled cholera toxin to determine the percentage
of G.sub.M1 to be included in the membrane for cholera toxin
binding assays. It was determined through fluorescence microscopy
that 1 mole percent is an acceptable concentration. This result was
confirmed on a MembraneChip.TM. surface detector device. See
Example 2 (supra) and FIG. 4.
[0121] Spreading solutions were created by adding 12.5 .mu.l of the
vesicle preparation to 12.5 .mu.l PBS buffer, and membrane chips
were produced on 12 mm-diameter circular cover glass (thickness 1.5
mm). Seven different samples were created, and placed under water
in separate wells of a 12-well plate (component percentages are
stated as mole percentages):
[0122] 1. 99% egg PC with 1% NBD-PG, unprobed
[0123] 2. 98% egg PC, 1% NBD-PG, and 1% G.sub.M1, unprobed
[0124] 3. 98% egg PC, 1% NBD-PG, and 1% G.sub.M1, probed with
labeled cholera toxin
[0125] 4. 98% egg PC, 1% NBD-PG, and 1% G.sub.M1, probed with
unlabeled cholera toxin
[0126] 5. 99% egg PC and 1% BODIPY-labeled G.sub.M1, unprobed
[0127] 6. 99% egg PC and 1% BODIPY-labeled G.sub.M1, probed with
labeled cholera toxin
[0128] 7. 99% egg PC and 1% BODIPY-labeled G.sub.M1, probed with
unlabeled cholera toxin
[0129] After aspirating away the excess water in the wells, each
was washed once with PBS and then was incubated in either 1 ml PBS
(samples 1, 2 and 5, supra) or a solution of 998 .mu.l PBS/2 .mu.l
cholera toxin (labeled [samples 3 and 6] or unlabeled [samples 4
and 7], depending on sample descriptions above). Plates were
covered with aluminum foil, and left on a rocking shaker for 1
hour. After the hour, each well was washed six times with 1 ml of
PBS per wash.
[0130] Each sample was removed from the 12-well plate while under
water, and moved to a dimpled slide for observation on the upright
fluorescence microscope (Nikon Instruments, Inc., Nikon Eclipse
E400, Melville, N.Y.). Throughout this manipulation and during the
data capture described below, samples were covered with a bulk
aqueous phase. ImagePro Plus (Version 4.5.0.19, Media Cybernetics,
Inc, Silver Spring, Md.) and CoolSnap (Version 1.1, Roper
Scientific, Inc., Tucson, Ariz.) software were used to capture
images. Tests were run on each sample to determine fluorescence
recovery after photobleaching (FRAP).
[0131] An approximately 100 micron diameter spot was photobleached
by a 60 second illumination with a 10.degree. W mercury arc lamp
(Ushio Inc., USH-102DH, Tokyo, Japan) directed through the aperture
diaphragm. This was immediately followed by a photograph taken
through the 20.times. objective, using FITC filter set appropriate
for the fluorescent label to be imaged. A five minute dark
"recovery period" followed the initial photograph. A final
photograph was taken immediately following the "recovery period"
and was compared to the first to determine the extent of
fluorescence recovery after photobleaching.
[0132] Results:
[0133] All of the unprobed samples (i.e., samples 1, 2 and 5)
showed dramatic recovery of fluorescence after photobleaching. See
discussion regarding FIGS. 5A and 5B, below. Sample number 3,
incubated with labeled cholera toxin, illustrated slightly greater
rates of recovery under the FITC filter (observing the NBD-PG
lipids) than under the Texas Red filter (Chroma, 30014808TXRD,
Brattleboro, Vt.) (which visualizes the cholera toxin which has
bound G.sub.M1). Data not shown. In both samples incubated with
labeled cholera toxin (i.e. samples 3 and 6), the photographs taken
with the FITC filter were tinted red, a result of the cholera
toxin's red fluorescence traveling through the long-pass filters
used on the microscope. Data not shown.
[0134] In the samples involving BODIPY-labeled G.sub.M1 (i.e.,
samples 5, 6, and 7), fluidity was high prior to binding of cholera
toxin to the membrane, and was significantly decreased after
incubation with either labeled or unlabeled cholera toxin. FIGS. 5A
and 5B illustrate results from a "minus cholera toxin" control
illustrating fluidity of the BODIPY-labeled G.sub.M1 membrane
component. FIG. 5A shows the photograph of sample 5 immediately
following photobleaching. An area of bleached BODIPY-labeled
G.sub.M1 is evident. FIG. 5B shows the same sample following the
five minute recovery period. Note the extensive diffusion of the
bleached fluorophore, resulting in fluorescence recovery of the
original bleached area.
[0135] FIGS. 5C and 5D show the results obtained with sample 7,
which was probed with unlabeled cholera toxin. Following
illumination, a well-defined area of bleached BODIPY-labeled
G.sub.M1 is evident. FIG. 5C. The bleached area remains well
defined following the five minute recovery period. FIG. 5D.
[0136] Discussion:
[0137] This experiment illustrates that supported lipid bilayers of
the present invention can be used to detect ligand binding without
direct observation of the ligand. By examining the effects of
molecule binding on the physical properties of the membrane, it is
possible to make well-informed deductions about membrane-molecule
interactions without reliance upon fluorophore-conjugated
ligands.
[0138] Particularly when comparing samples 5 and 7, illustrated
above, the differences in fluorescence recovery are clear. Because
recovery is a direct result of lateral fluidity of the labeled
membrane components, the results show that the G.sub.M1 molecules
lose mobility when bound to cholera toxin. Sample 3, which shows
greater fluorescence recovery under the green filter than the red,
suggests that unbound membrane components like NBD-PG may stay
relatively fluid while the lateral mobility of G.sub.M1 is
diminished following cholera toxin binding. Of course, standard
techniques such as fluorescence anisotropy (see, e.g., Lackowicz,
Principles of Fluorescence Spectroscopy, Kluwer Academic/Plenum:
New York (1999) (incorporated by reference)), and fluorescence
correlation spectroscopy (FCS) (see, e.g., Hess, et al., 2002) also
may be used to obtain information about changes in membrane
fluidity or acyl chain mobility. Libraries of compounds may be
screened to identify agents that interfere with binding of cholera
toxin to G.sub.M1. Libraries of compounds may comprise, e.g.,
combinatorial small molecule libraries, combinatorial biological
libraries such as combinatorial peptide or nucleic acid libraries,
or any other type of random or non-random group of compounds that
may be employed using the methods of the present invention. Such
compounds will block or diminish the cholera toxin-induced
alteration in G.sub.M1 lateral mobility, and can serve as lead
compounds for antibiotic development. Alternatively, a
combinatorial library containing, for example, polyenes,
lipopeptides, or cationic peptides, may be screened against an
array of microbial specific membrane components to identify lead
compounds for antibiotic development.
Example 4
Electrophoretic Detection of Ligand Binding-Induced Changes in
Membrane Fluidity
[0139] As described in detail in Example 3, the binding of cholera
toxin subunit B can be detected by the decrease in fluidity of
ganglioside G.sub.M1. In Example 3, fluidity changes, indicative of
ligand binding, were measured by fluorescence recovery after
photobleaching (FRAP). Electrophoresis is an alternate method for
measuring fluidity and fluidity in a membrane comprising a charged
component. As such, electrophoretic mobility changes can be used to
monitor ligand binding to one or more membrane components.
[0140] When an electric field is applied to a fluid membrane the
charged components experience a force. If a component of the force
is oriented within the plane of the membrane, the components will
migrate within the membrane plane to their isoelectric point, as
illustrated in FIG. 2 and diagramed in FIG. 6 (and also reviewed in
Groves J. T., and Boxer S. G., 2002 (incorporated by
reference)).
[0141] The migration is indicative of membrane fluidity, and can be
observed as, e.g., a concentration profile oriented along the
component of the field that lies within the plane of the membrane.
The concentration profile is easily detected using a labeled lipid,
as described in Example 1, supra and illustrated in FIG. 2.
[0142] A surface detector array device of fluid membrane targets
labeled with the same or different fluorophores is depicted in FIG.
6A. The array may contain identical lipid components, or,
alternatively, different corrals may contain different lipid
components. At least one component bears a net charge at the pH of
the bulk solution that overlays the array. One or more of these
arrays may be placed at the bottom of a well adapted for membrane
electrophoresis.
[0143] FIG. 7 illustrates a well adapted for this purpose. That
well may comprise one well within a multi-well plate assembly. The
well comprises a wall, 701, and a bottom surface, 702, that
together contain fluid, along with a pair of electrodes, 703, and
704. In one embodiment, electrodes, 703 and 704 comprise
uninsulated wires within the confines of the well. A surface
detector array device is placed within the well, and the portions
of electrodes 703 and 704 outside of the well are connected to a
power supply. The fluid within the well comprises conducting
species, i.e. ions, to carry current between the uninsulated
portions of electrodes 703 and 704. The surface detector device
intercepts the electric field, E, that runs between electrodes 703
and 704, so that any charged membrane component experiences a force
proportional to the charge, q, and the electric field, E. This
force causes the charged component to move, or electrophorese.
[0144] In an alternate embodiment, the electrodes, 703 and 704 are
adapted for electrically contacting electrode leads on a surface
detector device. The electrodes within the surface detector device
are preferably oriented to set up a field, E, that runs across the
corrals. This is conveniently accomplished by having the leads in
electrical contact with a conductor oriented on opposite sides of a
corral. Fabrication of surface detector devices comprising
electrodes is described in Section III, supra. The connection
between electrodes. 703 and 704, and the leads of a surface
detector device can be engineered so that most or all of the
current flows through a path that originates at one of the
electrodes 703 or 704, proceeds across the upper surface of the
surface detector device, and returns through the other of the
electrodes 703 or 704. B) minimizing current shunting along a
direct path between electrodes 703 and 704, current draw and joule
heating are kept to a minimum, and the electric field may be
optimally oriented to electrophorese supported bilayers contained
within the corrals.
[0145] This configuration can be engineered by, e.g., having
electrodes 703 and 704 comprise insulated wires and by having leads
on the bottom of the detector capable of making electrical contact
with the electrodes by piercing or cutting the insulation on
electrodes 703 and 704. Current shunting can be further minimized
by locating the leads within flexible O-rings or gaskets that form
a liquid tight seal between the electrodes 703, 704 and associated
lead assemblies and the fluid located within the well.
[0146] The surface detector array device is exposed to an electric
field, E, and in response, charged components within the membrane
electrophorese. If the charged components are labeled with, e.g., a
fluorophore or other dye, the electrophoresis can be detected as a
concentration gradient of that label. FIG. 6B. In other
embodiments, the charged component is unlabeled and its movement
induces the movement of an uncharged, labeled component such as by,
e.g., viscous drag.
[0147] In one advantageous experimental setup, an array configured
for membrane electrophoresis comprises distinct membrane
compositions in different corrals. Each corral comprises a charged
and labeled membrane component to facilitate electrophoretic
membrane fluidity measurements. The array is exposed to a compound
library (e.g., combinatorial small molecule libraries,
combinatorial biological libraries such as combinatorial peptide or
nucleic acid libraries, or any other type of random or non-random
group of compounds that may be employed using the methods of the
present invention) wherein the compounds preferably are not
labeled. FIG. 6C. A library compound binds a membrane target within
the array. The array is subjected to an electric field, E. The
binding of a library compound to a membrane target alters the
membrane fluidity. This binding is detected as an alteration in the
usual electrophoretically-induced concentration gradient of the
labeled membrane component. FIG. 6D, corral 60 highlighted in
green. An image of the surface detector array device may be
obtained using, e.g., a captured fluorescence image, and
software-driven analysis may be used to detect the binding event.
For low-throughput embodiments, the binding event may be detected
visually by direct observation of the MembraneChip.TM. through a
fluorescence microscope.
Example 5
Membrane-Based Assays for Antibiotic Development
[0148] Bacterial strains that are resistant to antibiotic treatment
create a global health concern that rapidly is increasing in
severity. Gonorrhea's growing resistance to fluoroquinolones, for
example, has resulted in the loss of half of the nation's
first-line anti-gonorrheal arsenal. Some forms of gonorrhea also
are building intermediate resistance to cephalosporin drugs. These
multi-resistant strains originate from antibiotic abuse in East
Asia and already have appeared in Hawaii and California.
[0149] One of the problems with bacteria-targeting antibiotics is
that only a few major classes of drugs exist, as illustrated in
Table 1:
TABLE-US-00001 TABLE 1 Classes of antibiotics that target bacteria
and their mechanisms of action. Drug Class Action .beta.-Lactams,
Inhibit peptidoglycan synthesis Cephalosporins Aminoglycosides,
Inhibit protein synthesis Macrolides, Tetracyclines
Fluoroquinolones Inhibit DNA gyrase
[0150] Bacteria that become resistant to any one of the
fluoroquinolones usually become resistant to the entire class.
Antibiotic resistance is exacerbated by over prescription, failure
to complete the full course of treatment, and ubiquity in
agricultural use. Improperly used, antibiotics harm populations
while conferring small benefits to individuals.
[0151] Historically, most antibiotics were designed to target
microbial biochemical pathways. Pathways are easy to study in vitro
since enzyme inhibition assays are well developed and quantitative
models exist for the data. Targeting pathways in intact
microorganisms is difficult, however, because of the cell wall.
"Getting a potential drug past the cell membrane to reach its
target is a huge challenge and one that we often fail at," says
pharmaceutical chemist Gordon Amidon. Science 296: 838 (2002).
[0152] Even more important, the strategy of inhibiting pathways
(peptidoglycan or protein synthesis; DNA replication) with
antibiotics does not always kill the cell. Instead, the
microorganism's growth may only be slowed down, leaving a chance
for resistance to develop by horizontal evolution. This process of
gene exchange among nearby bacterial cells occurs by transduction,
transformation and conjugation. Of course, resistance genes are
also passed down to bacterial progeny by vertical evolution.
Together the two modes of evolution make bacteria a formidable
enemy.
[0153] Microorganisms capable of causing life-threatening
infections possess a number of membrane structures vital to their
survival and pathogenesis, but are nevertheless absent from the
human host. The MembraneChip.TM. surface detector array devices are
ideally suited for displaying arrays of microbe-specific membrane
targets in their native membranes (lipid bilayers). Many of these
membrane targets already have been pharmaceutically validated since
they are the end products of biosynthetic pathways that are
targeted by existing therapeutics. For example, mycolic acid and
ergosterol may be considered pharmaceutically-validated membrane
targets based on the mechanism of action of existing drug
therapies. Mycobacteria are named for their characteristic
possession of the long chain fatty acid mycolic acid in their cell
walls, which is necessary for the viability of these organisms, but
is not present in human membranes. Isoniazid is a first line
antibiotic against Mycobacterium tuberculosis. This synthetic
analog of pyridoxine is thought to perturb the assembly of mycolic
acids by inhibiting the enzymes responsible for their synthesis.
Another integral membrane component unique to fungi but not present
in human is ergosterol. The anti-fungal activity of the more recent
synthetic drugs (e.g., fluconazole, ketoconazole) is attributed to
their inhibition of the biosynthesis of ergosterol.
[0154] Gram-negative bacteria possess a lipopolysaccharide specific
to their cell wall, called endotoxin. Mammalian cells possess
certain glycolipids in their membrane, similar in structure to, but
not exactly the same as endotoxin. Having membranes containing
endotoxin (target) and mammalian glycolipids (anti-target)
represented within an array, preferably, in adjacent array
elements, allows for optimization of drugs that preferentially bind
the target and not the anti-target. Target specificity is key to
antibiotic drug discovery as many efficacious drugs have grave
safety issues. One important advantage of targeting the membrane is
that membrane therapeutics act immediately and do not have to cross
the microbial cell membrane. Targeting the membrane also has
another significant benefit. Stalling cell growth by inhibiting
peptidoglycan and/or protein synthesis and/or DNA replication
allows for horizontal evolution via gene exchange among nearby
bacterial cells. By contrast, killing cells upon immediate membrane
contact makes the creation of resistant strains far more
difficult.
[0155] Sepsis is a systemic response to infection that can lead to
septic shock, a catastrophic syndrome characterized by refractory
hypotension and multiple organ failure. In the United States half a
million patients are annually affected with fatality rates up to
40%. No approved pharmaceutical therapy exits for sepsis and septic
shock.
[0156] Sepsis is caused by endotoxins, complex lipopolysaccharides
(LPS) present in the cell walls of all Gram-negative bacteria. The
basic endotoxin consists of two distinct regions: a hydrophobic
polysaccharide, which includes an O-specific side chain and an
inner and outer core region, and the hydrophobic toxic lipid A
component. Lipid A is highly conserved across bacterial
families.
[0157] Endotoxin can enter the blood by two methods: 1) through
local or systemic infection by exogenous Gram-negative bacteria,
and 2) by translocation of endogenous Gram-negative bacteria from
the intestinal membrane especially after systemic insults.
Circulating endotoxin can stimulate reactions from the immune
system and tissue cells to induce an overwhelming inflammatory host
response, resulting in the clinical syndrome know as "sepsis".
[0158] The surface detector array devices or MembraneChips.TM.
described above are used to screen for agents that selectively bind
bacterial membrane targets such as endotoxins but not to human
orthologues. These agents may be used as antibiotics, or as lead
compounds for antibiotic development. Highly multiplexed assays may
be carried out by placing surface detector array devices (i.e.,
MembraneChips.TM.) in the bottoms of the wells of a standard
multiwell plate. A different compound (i.e., test agent) or
different groups of compounds may be placed in each well to assay
the interaction between the test agent(s) and the target
compositions. In a preferred embodiment, different endotoxin forms
(i.e., targets) derived from different bacteria are displayed as
array elements within corrals, along with control membrane samples
(anti-targets) derived from one or more mammalian sources that may
comprise different tissues and/or different species to assure
selective targeting.
[0159] The surface detector array devices or MembraneChips.TM. are
compatible with scanning by atomic force microscopy (AFM) or any
other types of scanning probe microscopy, such as lateral force
microscopy, and chemical force microscopy. For some microscopes,
minor modifications to the stage assemblies may be required to
accommodate the device. Most importantly, the microscope must be
adapted for use with a sample in contact with a fluid because the
surface of the surface detector array device must remain covered
with bulk fluid. Such microscopes are known to persons of skill in
the art and are described in, e.g., U.S. Pat. No. 5,949,070 to
Gamble, incorporated herein by reference. The visualization of
lipid bilayer membrane structures gives a better understanding of
biological processes, such as distribution of the membrane target,
binding properties of membrane target to drug, membrane appearance,
membrane continuity, membrane integrity, membrane thickness,
membrane bending modulus, and membrane tension. Atomic force
microscopy (AFM) or other types of scanning probe microscopy, such
as lateral force microscopy, or chemical force microscopy already
have been utilized to detect ultralow forces, such as
receptor-ligand interactions (see, e.g., Florin, et al., 1994,
incorporated by reference) or single molecule-level
antibody-antigen interactions (see, e.g., Schwesinger, et al. 2000,
incorporated by reference). Atomic force microscopy (AFM) or other
types of scanning probe microscopy, such as lateral force
microscopy, or chemical force microscopy therefore can be used in
the practice of the invention methods to detect binding of agents
to membrane components and/or membrane disruption resulting from
agent binding.
[0160] Materials and Methods
[0161] Naturally occurring endotoxins are complex
lipopolysaccharides (LPS) in the cell wall of all Gram-negative
bacteria. Different naturally occurring lyophilized LPSs, (for
example, wild type LPS, rough mutant LPS, and deep rough mutant
LPS) are personal gifts from Thomas Gutsmann and Ulrich Seydel,
Borstel Institute. Different lyophilized LPSs are first dissolved
in 65:25:4 chloroform:methanol:deionized water. They then are
combined with different composition of lipids (including, for
example, phosphatidylcholine, phosphoethanolamine,
phosphotidylglycerol, phosphatidylserine, phosphatidylinositol,
cholesterol, sphingomyelin, etc.) dissolved in the chloroform
mixture to make a homogeneous mixture. The solvent is evaporated
from the lipid mixture by a rotary evaporators (Buchi Rotary
Evaporators, C Assembly). The remaining lipid cake is hydrated over
night with deionized water at 4.degree. C. to form multilamellar
vesicles. The multilamellar vesicles are resuspended in deionized
water and then extruded above the T.sub.c temperature to form small
unilamellar vesicles.
[0162] These vesicles then are arrayed out onto MembraneChips.TM.
at the bottom of standard well plates by suing a membrane arrayer.
This procedure is described in detail in U.S. application Ser. No.
10/200,682, filed Jul. 22, 2002 (attorney docket number
23604-7001). The resulting MembraneChips.TM. are used to screen
combinatorial peptide or other chemical libraries.
[0163] The library of compounds is screened to identify agents that
selectively bind the microbial membrane components using direct or
displacement binding assay methods such as those outlined in U.S.
application Ser. No. 10/200,682, filed Jul. 22, 2002 (attorney
docket number 23604-7001), or a membrane fluidity-based assay such
as is described in Examples 3 and 4, supra. For fluidity-based and
displacement assays, the library, which preferably includes small
molecules that self assemble to destroy microbial membranes,
polyenes, lipopeptides, and cationic peptides, may comprise
unlabeled agents. Agents that selectively bind microbial but not
mammalian membrane components comprise lead compounds that may then
be tested for antibiotic activity and, if necessary, optimized to
refine activity, pharmacokinetics, pharmacodynamics and
side-effects profile using techniques standard in the
pharmaceutical chemical arts.
[0164] Furthermore, biological libraries can be screened not only
to identify agents that bind to the intended target but also to
identify agents that disrupt membranes. Membrane disrupting agents
may be identified by measuring voltage and capacitance differences
(see, e.g., Sackmann and Tanaka, 2000; Cornell, et al., 1997,
incorporated by reference).
Example 6
Membrane Fluidity Assay
[0165] The mobility of a ligand (cholera toxin), its membrane
target (ganglioside GM1), and non-participating background lipid
during multivalent binding on fluid membrane surfaces was examined.
Experiments were performed using supported membrane microarrays.
Supported membranes were assembled by spontaneous adsorption and
fusion of unilamellar vesicles onto clean silica surfaces which had
been photolithographically patterned with chrome grids. The chrome
creates surface barriers that isolate the individual membrane
corrals.
[0166] Robotic direct dispensing methods with Cartesian MicroSysTM
Model 4100-2SQ were employed to deposit 40 nl droplets of vesicle
suspension into the pre-patterned 500.times.500 .mu.m corrals.
Vesicle fusion occurred within seconds of deposition, forming fluid
supported membranes that continuously filled each corral (FIG. 8A).
Membrane fluidity was monitored by fluorescence recovery after
photobleaching (FRAP) of the fluorescent probe lipid (NBD-PG).
Fluid membranes exhibit diffusion coefficients typically ranging
from 1-5 .mu.m.sup.2/s with no detectable immobile fraction.
[0167] Binding of CTB to GM1-containing supported membranes was
readily observed using fluorescently labeled CTB (Alexa Fluor.RTM.
594 conjugate). Quantitative studies over a range of CTB
concentrations reveal an average KD of 13.2 nM (see Example 7), in
agreement with known values. Whereas the membranes are fully fluid
prior to CTB binding, fluidity is significantly attenuated
afterwards. FRAP experiments were performed by minimizing the
microscope aperture to illuminate a small (100 .mu.m diameter)
region in the center of the corral. The excitation light
substantially photobleaches fluorescent probes within this region
in 60 s. After 10 minutes, the photobleached pattern was imaged
again, quantifying the rate of diffusive mixing. Results from
experiments on labeled CTB, labeled GM1, and labeled lipid (NBD-PG)
are summarized in FIG. 8B.
[0168] Observations of labeled CTB indicate that it is relatively
immobile when bound to supported membranes. The large size and
multivalent binding of CTB likely contribute to this reduced
mobility. A corresponding set of experiments, utilizing labeled GM1
(BODIPY FL C5) and unlabeled CTB, were performed to characterize
the mobility of GM1 during CTB binding. Before exposure to CTB,
labeled GM1 exhibits lateral diffusion, though somewhat attenuated
relative to other lipids, perhaps as a result of slight aggregation
(FIG. 8B). After CTB binding, a substantial reduction in the
diffusion rate of labeled GM1 (now complexed with CTB) was
observed.
[0169] A most interesting feature of these experiments is revealed
when the mobility of the lipid probe (NBD-PG) is monitored during
CTB-GM1 binding. Despite the fact that this lipid does not
participate in the binding interaction, its mobility is markedly
affected. FRAP experiments on the 1 mol % NBD-PG in DMPC/GM1
(98.75/0.25 mol %) membranes reveal a drastic reduction in mobility
in conjunction with CTB binding. (The GM1 target concentration used
in these experiments is 20-fold lower than the 5 mol % GM1 reported
as the minimum required for analyzable kinetic data using a Biacore
surface plasmon resonance system. Kuziemko et al., Biochemistry
1996, 35, 6375-6384.) Data from FRAP experiments are shown in FIG.
8B and a schematic of this system is drawn in FIG. 9. Similar
experiments, performed using egg-PC (a natural mixture of PCs
containing .about.50% unsaturated fatty acids) instead of the
saturated DMPC, did not show a reduction in NBDPG mobility
associated with CTB-GM1 binding (FIG. 8B). The independence of
NBD-PG mobility from CTB-GM1 binding in egg-PC membranes confirms
that NBD-PG has no intrinsic interaction with CTB or GM1. An
important difference between egg-PC and DMPC membranes is the
gel-fluid transition temperature of DMPC (23.degree. C.), which is
much higher than that of egg-PC. Proximity to a gel-fluid
transition may contribute to the mobility effect observed in the
DMPC system.
Example 7
Binding Affinity on a Chip
[0170] Vesicles with increasing concentrations of GM1 (0%, 0.01%,
0.05%, 0.15%, 0.25%, 0.5%, 1%, 2%) with 1% NBD-PG in egg PC were
robotically dispensed with Cartesian MicroSysTM Model 4100-2SQ.
Direct dispensing methods were employed to deposit (10 nl) each of
the 8 vesicle suspensions into pre-patterned 250.times.250
.mu.m.sup.2 corrals in a row. Vesicle fusion occurs within seconds
of deposition, forming fluid supported membranes that continuously
fill each corral. Membrane fluidity was monitored by fluorescence
recovery after photobleaching (FRAP) of the fluorescent probe lipid
(NBD-PG). Eight identical chips were exposed to 8 increasing
concentrations of Cholera Toxin B (0 nM, 5 nM, 10 nM, 20 nM, 30 nM,
50 nM, 100 nM, 300 nM). Curve fitting to one site binding,
Y=Bmax*X/(Kd+X), (Prism 3.0, GraphPad Software Inc., San Diego,
Calif.) yielded an average binding constant of 13.2 nM at 0.25% GM1
from 3 independently performed experiments.
[0171] While the invention has been described with reference to
specific methods and embodiments, it will be appreciated that
various modifications may be made without departing from the
invention. All references cited, including scientific publications,
patent applications, and issued patents, are herein incorporated by
reference in their entirety for all purposes.
REFERENCES
[0172] Barenholz, Y., et al., Biochemistry 16:2806-2810 (1977).
[0173] Binnig, G., Quate, C. F., and Gerber, C, Phys. Rev. Lett.
56:930-933 (1986). [0174] Clegg, R. E., "Fluorescence Resonance
Energy Transfer" (Chapter 7) in X. F. Wang and B. Herman, (eds.),
Fluorescence Imaging Spectroscopy and Microscopy, Chemical Analysis
Series, vol. 137, pp. 179-252, Wiley-Interscience, New York (1996).
[0175] Colchero, J., Bielefeldt, H., Ruf, A., Hipp, M., Marti, O.,
and Mylnek, J., Phys. Stat. Sol. (a) 131:73-75 (1992). [0176]
Groves, J. T., and Boxer, S. G., Acc Chem Res 35(3): 149-57 (2002).
[0177] Cornell, B. A., et al., Nature 387:580-583 (1997). [0178]
Elender, et al., Biosensors and Bioelectronics 11:565-577 (1996).
[0179] Florin, E.-L., Moy, V. T. and Gaub, H. E., Science
264:415-417 (1994). [0180] Frisbie, C. D., Rozsnyai, L. F., Noy,
A., Wrighton, M. S., and Lieber, C. M., Science 265:2071-2074
(1994). [0181] Griffiths, P. R. and de Haseth, J. A.,
Fourier-Transformed Infrared Spectrometry, John Wiley, New York,
(1986). [0182] Groves, J. T., and Boxer, S. G., Biophys. J. 69:1972
(1995). [0183] Groves, J. T., et al., Biophys. J. 71:2716 (1996).
[0184] Haugland, R. P., in HANDBOOK OF FLUORESCENT PROBES AND
RESEARCH CHEMICALS, 5th Ed., Molecular Probes, Inc., Eugene, Oreg.
(1992). [0185] Hess, S. T., Huang, S., Heikal, A. A., and Webb, W.
W., Biochemistry 41(3):697-705 (2002). [0186] Hillebrandt H.,
Wiegand, G., et al., Langmuir 15:8451-8459 (1999). [0187] Hillner,
P. E., Radmacher, M., and Hansma, P. K., Scanning 17:144-147
(1995). [0188] Hu, J., Li, Ls, Yang W., Manna L., Wang L. W., and
Alivisatos A. P., Science 292(5524):2060-3 (2001).
[0189] Khuner, et al., Biophys J. 67:217-226 (1994). [0190] Kim,
J., Kim, G., and Cremer, P. S., J Am Chem Soc. 124(29):8751-6
(2002). [0191] Krutenat, Kirk-Othmer 3rd Ed., Vol. 15, pp. 241-274
(1986). [0192] Lackowicz, Principles of Fluorescence Spectroscopy,
Kluwer Academic/Plenum: New York (1999). [0193] Lipowsky, R., and
Sackmann, E., STRUCTURE AND DYNAMICS OF MEMBRANES, Elsevier,
Amsterdam (1995). [0194] Martin, F. J., in SPECIALIZED DRUG
DELIVERY SYSTEMS--MANUFACTURING AND PRODUCTION TECHNOLOGY, (P.
Tyle, Ed.) Marcel Dekker, New York, pp. 267-316 (1990). [0195]
Tamm, L. K., and Kalb, E., "Microspectrofluorimetry Of Supported
Planar Membranes," in MOLECULAR LUMINESCENCE SPECTROSCOPY (S. G.
Schulman, Ed.) John Wiley & Sons, Inc., pp. 253-305 (1993).
[0196] Taton T. A., Lu G., and Mirkin C. A., J Am Chem Soc.
123(21):5164-5 (2001). [0197] Salafsky, J., Groves, J. T., and
Boxer, S. G., Biochem. 35:14773-14781 (1996). [0198] Sackmann E.,
Tanaka M., Trends Biotechnol. 18(2):58-64 (2000). [0199] Safran,
S., STATISTICAL THERMODYNAMICS OF SURFACES INTERFACES, AND
MEMBRANES, Addison-Wesley Publishing Company (1994). [0200]
Schwesinger, F., Ros, R., et al., Proc. Natl. Acad. Sci. (USA)
97:9972-9977 (2000). [0201] Wolf, S., and Tauber, R. N., SILICON
PROCESSING FOR THE VLSI ERA, Vol. 1, Lattice Press, Sunset Beach,
Calif. (1986). [0202] Wong, A. P., and Groves, J. T., J Am Chem
Soc. 123(49): 12414-5 (2001). [0203] Xia, Y., et al., Science
273:347 (1996). [0204] Yin, Y. L. and Hyde, J. S., J Chem Phys
91:6029-6035 (1989).
* * * * *
References